Using transcriptomic data to refine molecular interpretation in laboratory cancer testing​

Speaker: Dr. rer. nat. Tobias Bethge, Genetica AG, Zurich, Switzerland​

About this webinar​

Variants of uncertain significance (VUS) remain one of the most persistent bottlenecks in hereditary cancer testing - particularly those located near splice sites, in non-coding regions, or affecting copy number. In this talk, Tobias Bethge shares how Genetica AG, a genetic counseling and diagnostics laboratory in Zurich, has incorporated targeted RNA sequencing alongside DNA-based testing to functionally resolve such variants.​

Tobias opens with the practical groundwork: how RNA-seq can functionally interrogate variants predicted to affect splicing, how it can indirectly flag deep intronic, regulatory, and structural events that DNA sequencing alone may miss, and the real constraints labs face - from limited gene expression in accessible tissues, to the sampling and library preparation decisions that shape data quality. He then introduces a targeted capture-panel approach developed in collaboration with SOPHiA GENETICS, built around an 18-gene RNA panel spanning the lab's broader 83-gene hereditary cancer panel, designed to enrich relevant transcripts while reducing background and sequencing cost.​

The talk is grounded in four real test cases from Genetica's cohort. A BRCA2 missense variant at the edge of an exon boundary is shown to cause exon skipping in roughly half of transcripts - supporting a pathogenic classification. Two non-coding BRCA1 variants near exon 1 illustrate how seemingly similar splice-site predictions can resolve very differently: one shown to be a benign splicing polymorphism also present in controls, the other showing partial allelic loss consistent with a likely pathogenic, possibly hypomorphic effect - a distinction made possible by tracking heterozygous SNPs across DNA and RNA. A final case demonstrates how RNA-seq can confirm that a PALB2 exon 11 duplication detected by CNV analysis and MLPA sits in tandem and disrupts the reading frame, supporting a pathogenic call.​

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You will learn:​

• How RNA-seq complements DNA sequencing by functionally testing splicing-related VUS and indirectly detecting deep intronic or regulatory events​
• Key sampling and library preparation tradeoffs - PAXgene blood tubes vs. cultured cells vs. tissue biopsy, and capture-panel vs. whole-transcriptome approaches​
• How a targeted RNA capture panel, developed with SOPHiA GENETICS, enriches relevant transcripts while reducing sequencing cost and background noise​
• How sashimi plots and control sample comparisons distinguish pathogenic splicing disruption from natural splicing polymorphisms​
• How heterozygous SNP tracking across DNA and RNA can reveal allele-specific expression loss​
• How transcript-level analysis can confirm whether a structural variant, such as an exon duplication, disrupts the reading frame​
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SOPHiA DDM™ applications and Alamut™ Visual Plus are For Research Use Only unless otherwise specified. The RNA-seq capture panel solution discussed is part of an ongoing research collaboration and is not yet commercially available. The opinions expressed are those of the speaker and may not represent the opinions of SOPHiA GENETICS.​

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